i'd check for RF interference since that is almost always the cause of issues with the MRF350.

start by setting your dial on the bottom to zero (if it's already at zero, then that is an issue).  Once it is set to zero, look at the status lights on the RFX250 antenna.  If the status light is blinking without pressing buttons on the remote, you are getting interference.  Find a location for the antenna that doesn't blink the RF status light.  Then turn the dial back to match what is in your programming file.

Next step, do you have your IR routing set up correctly or do you just have it set to all outputs for your emitters?

next step if the above items don't help.

try setting the IR routing to be IR only from the remote.  Point your remote at the devices.  Does it control the devices correctly?